Genome Resources for Seven Fungal Isolates That Cause Dollar Spot Disease in Turfgrass, Including <i>Clarireedia jacksonii</i> and <i>C. monteithiana</i>

Crouch, Jo Anne; Beirn, Lisa A.; Boehm, Michael J.; Carbone, Ignazio; Clarke, Bruce B.; Kerns, James P.; Malapi‐Wight, Martha; Mitchell, Thomas K.; Venu, R. C.; Tredway, Lane P.

doi:10.1094/pdis-06-20-1296-a

Cited by 6 publications

(16 citation statements)

References 20 publications

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“…Next generation sequencing (NGS) allows for rapid sequencing and identification of pathogens through complete genome sequencing [ 90 ]. Next generation sequencing is used for drafting genomes of pathogens or to discover single nucleotide polymorphisms (SNPs) and single nucleotide variants (SNVs) in a sample [ 91 , 92 , 93 , 94 , 95 ]. This information can be used to determine the pathogen race or lineage [ 93 ].…”

Section: Nucleic Acid-based Techniquesmentioning

confidence: 99%

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Turfgrass Disease Diagnosis: Past, Present, and Future

Stackhouse

Martínez-Espinoza

Ali

2020

Plants

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Turfgrass is a multibillion-dollar industry severely affected by plant pathogens including fungi, bacteria, viruses, and nematodes. Many of the diseases in turfgrass have similar signs and symptoms, making it difficult to diagnose the specific problem pathogen. Incorrect diagnosis leads to the delay of treatment and excessive use of chemicals. To effectively control these diseases, it is important to have rapid and accurate detection systems in the early stages of infection that harbor relatively low pathogen populations. There are many methods for diagnosing pathogens on turfgrass. Traditional methods include symptoms, morphology, and microscopy identification. These have been followed by nucleic acid detection and onsite detection techniques. Many of these methods allow for rapid diagnosis, some even within the field without much expertise. There are several methods that have great potential, such as high-throughput sequencing and remote sensing. Utilization of these techniques for disease diagnosis allows for faster and accurate disease diagnosis and a reduction in damage and cost of control. Understanding of each of these techniques can allow researchers to select which method is best suited for their pathogen of interest. The objective of this article is to provide an overview of the turfgrass diagnostics efforts used and highlight prospects for disease detection.

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Section: Nucleic Acid-based Techniquesmentioning

confidence: 99%

“…This technology has been utilized in turfgrass for full genome sequencing of Clarireedia spp. the dollar spot causing pathogens [ 95 ]. The development and application of these and other technologies will provide more efficient detection of turfgrass pathogens.…”

Section: Nucleic Acid-based Techniquesmentioning

confidence: 99%

Turfgrass Disease Diagnosis: Past, Present, and Future

Stackhouse

Martínez-Espinoza

Ali

2020

Plants

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“…The CAPS method was also examined in silico against the Clarireedia spp. sequences from Salgado-Salazar et al study and found that of the sixteen sequences in GenBank, all but one sample of C. jacksonii is expected to produce two bands [11]. That one sample had a point mutation within the restriction digest region.…”

Section: Discussionmentioning

confidence: 95%

“…The last two species, C. jacksonii and C. monteithiana, are found on grasses worldwide, including the US. Reclassification has rejuvenated research into this pathogen [11,12].…”

Section: Introductionmentioning

confidence: 99%

Development of a Co-Dominant Cleaved Amplified Polymorphic Sequences Assay for the Rapid Detection and Differentiation of Two Pathogenic Clarireedia spp. Associated with Dollar Spot in Turfgrass

et al. 2021

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Dollar spot is one of the most destructive diseases in turfgrass. The causal agents belong to the genus Clarireedia, which are known for causing necrotic, sunken spots in turfgrass that coalesce into large damaged areas. In low tolerance settings like turfgrass, it is of vital importance to rapidly detect and identify the pathogens. There are a few methods available to identify the genus Clarireedia, but none of those are rapid enough and characterize down to the species level. This study produced a co-dominant cleaved amplified polymorphic sequences (CAPS) test that differentiates between C. jacksonii and C. monteithiana, the two species that cause dollar spot disease within the United States. The calmodulin gene (CaM) was targeted to generate Clarireedia spp. specific PCR primers. The CAPS assay was optimized and tested for specificity and sensitivity using DNA extracted from pure cultures of two Clarireedia spp. and other closely related fungal species. The results showed that the newly developed primer set could amplify both species and was highly sensitive as it detected DNA concentrations as low as 0.005 ng/µL. The assay was further validated using direct PCR to speed up the diagnosis process. This drastically reduces the time needed to identify the dollar spot pathogens. The resulting assay could be used throughout turfgrass settings for a rapid and precise identification method in the US.

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“…These determinants were previously characterized in S. sclerotiorum (Xia et al, 2019), the closest fully sequenced and well characterized relative species to Clarireedia. LWC-10 and HRI11 (Green et al, 2016;Crouch et al, 2021), DRR09 and RB-19 (Crouch et al, 2021), H3 and H2 isolates, representative of C. jacksonii, C. monteithiana, and C. aff. paspali were used in this analysis.…”

Section: At the Genomic Levelmentioning

confidence: 99%

Whole genome sequencing of Clarireedia aff. paspali reveals potential pathogenesis factors in Clarireedia species, causal agents of dollar spot in turfgrass

Bahri

Parvathaneni²,

Spratling³

et al. 2023

Front. Genet.

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Dollar spot is one of the most damaging diseases in turfgrass, reducing its quality and playability. Two species, Clarireedia monteithiana and C. jacksonii (formerly Sclerotinia homoeocarpa) have been reported so far in the United States To study the Clarireedia genome, two isolates H2 and H3, sampled from seashore paspalum in Hawaii in 2019 were sequenced via Illumina paired-end sequencing by synthesis technology and PacBio SMRT sequencing. Both isolates were identified as C. aff. paspali, a novel species in the United States Using short and long reads, C. aff. paspali H3 contained 193 contigs with 48.6 Mbp and presented the most completed assembly and annotation among Clarireedia species. Out of the 13,428 protein models from AUGUSTUS, 349 cytoplasmic effectors and 13 apoplastic effectors were identified by EffectorP. To further decipher Clarireedia pathogenicity, C. aff. paspali genomes (H2 and H3), as well as available C. jacksonii (LWC-10 and HRI11), C. monteithiana (DRR09 and RB-19) genomes were screened for fifty-four pathogenesis determinants, previously identified in S. sclerotiorum. Seventeen orthologs of pathogenicity genes have been identified in Clarireedia species involved in oxalic acid production (pac1, nox1), mitogen-activated protein kinase cascade (pka1, smk3, ste12), appressorium formation (caf1, pks13, ams2, rgb1, rhs1) and glycolytic pathway (gpd). Within these genes, 366 species-specific SNPs were recorded between Clarireedia species; twenty-eight were non-synonymous and non-conservative. The predicted protein structure of six of these genes showed superimposition of the models among Clarireedia spp. The genomic variations revealed here could potentially lead to differences in pathogenesis and other physiological functions among Clarireedia species.

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Genome Resources for Seven Fungal Isolates That Cause Dollar Spot Disease in Turfgrass, Including Clarireedia jacksonii and C. monteithiana

Cited by 6 publications

References 20 publications

Turfgrass Disease Diagnosis: Past, Present, and Future

Turfgrass Disease Diagnosis: Past, Present, and Future

Development of a Co-Dominant Cleaved Amplified Polymorphic Sequences Assay for the Rapid Detection and Differentiation of Two Pathogenic Clarireedia spp. Associated with Dollar Spot in Turfgrass

Whole genome sequencing of Clarireedia aff. paspali reveals potential pathogenesis factors in Clarireedia species, causal agents of dollar spot in turfgrass

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